| 3 |
3 |
|
| 4 |
4 |
EAPI=8
|
| 5 |
5 |
|
| 6 |
|
inherit flag-o-matic toolchain-funcs
|
|
6 |
inherit toolchain-funcs
|
|
7 |
|
|
8 |
MY_PV="${PV/_beta/b}"
|
| 7 |
9 |
|
| 8 |
10 |
DESCRIPTION="Sequence analysis using profile hidden Markov models"
|
| 9 |
11 |
HOMEPAGE="http://hmmer.org/"
|
| 10 |
|
SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
|
|
12 |
SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
|
|
13 |
S="${WORKDIR}/${PN}-${MY_PV}"
|
| 11 |
14 |
|
| 12 |
|
LICENSE="GPL-2"
|
| 13 |
|
SLOT="2"
|
| 14 |
|
KEYWORDS="~amd64 ~x86"
|
| 15 |
|
IUSE="cpu_flags_ppc_altivec test"
|
|
15 |
LICENSE="GPL-3"
|
|
16 |
SLOT="0"
|
|
17 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
|
|
18 |
IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test"
|
| 16 |
19 |
RESTRICT="!test? ( test )"
|
| 17 |
20 |
|
|
21 |
RDEPEND="
|
|
22 |
mpi? ( virtual/mpi )
|
|
23 |
gsl? ( sci-libs/gsl:= )"
|
|
24 |
DEPEND="${RDEPEND}"
|
| 18 |
25 |
BDEPEND="test? ( dev-lang/perl )"
|
| 19 |
26 |
|
| 20 |
27 |
PATCHES=(
|
| 21 |
|
"${FILESDIR}/${P}-fix-perl-shebangs.patch"
|
| 22 |
|
"${FILESDIR}/${P}-fix-build-system-destdir.patch"
|
|
28 |
"${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch
|
|
29 |
"${FILESDIR}"/${PN}-3.1_beta2-makefile.patch
|
| 23 |
30 |
)
|
| 24 |
31 |
|
| 25 |
32 |
src_configure() {
|
| 26 |
|
# required to expose pthread_setconcurrency(), #882279
|
| 27 |
|
append-cppflags -D_XOPEN_SOURCE=500
|
| 28 |
|
|
| 29 |
|
# prevent stray environmental variable
|
| 30 |
|
# from causing issues in the test phase
|
| 31 |
|
unset TMPDIR
|
|
33 |
# make build verbose, bug #429308
|
|
34 |
export V=1
|
| 32 |
35 |
|
| 33 |
36 |
econf \
|
| 34 |
|
--enable-lfs \
|
|
37 |
--disable-pic \
|
| 35 |
38 |
--enable-threads \
|
| 36 |
|
$(use_enable cpu_flags_ppc_altivec altivec)
|
|
39 |
$(use_enable cpu_flags_ppc_altivec vmx) \
|
|
40 |
$(use_enable cpu_flags_x86_sse sse) \
|
|
41 |
$(use_enable mpi) \
|
|
42 |
$(use_with gsl)
|
| 37 |
43 |
}
|
| 38 |
44 |
|
| 39 |
45 |
src_compile() {
|
| 40 |
|
emake AR="$(tc-getAR) rcs"
|
|
46 |
emake AR="$(tc-getAR)"
|
| 41 |
47 |
}
|
| 42 |
48 |
|
| 43 |
49 |
src_install() {
|
| 44 |
50 |
default
|
|
51 |
dodoc Userguide.pdf
|
| 45 |
52 |
|
| 46 |
|
newlib.a src/libhmmer.a libhmmer2.a
|
| 47 |
|
insinto /usr/include/hmmer2
|
| 48 |
|
doins src/*.h
|
| 49 |
|
|
| 50 |
|
dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
|
| 51 |
|
dolib.a squid/libsquid.a
|
| 52 |
|
insinto /usr/include/hmmer2
|
| 53 |
|
doins squid/*.h
|
| 54 |
|
|
| 55 |
|
dodoc NOTES Userguide.pdf
|
| 56 |
|
newdoc 00README README
|
| 57 |
|
|
| 58 |
|
# rename files due to collisions with hmmer-3
|
| 59 |
|
# in order to make SLOTing possible
|
| 60 |
|
local i
|
| 61 |
|
|
| 62 |
|
# first rename man pages...
|
| 63 |
|
pushd "${ED}"/usr/share/man/man1/ >/dev/null || die
|
| 64 |
|
for i in hmm*.1; do
|
| 65 |
|
mv ${i%.1}{,2}.1 || die
|
| 66 |
|
done
|
| 67 |
|
popd >/dev/null || die
|
| 68 |
|
|
| 69 |
|
# ... then rename binaries
|
| 70 |
|
pushd "${ED}"/usr/bin/ >/dev/null || die
|
| 71 |
|
for i in hmm*; do
|
| 72 |
|
mv ${i}{,2} || die
|
| 73 |
|
done
|
| 74 |
|
popd >/dev/null || die
|
| 75 |
|
}
|
| 76 |
|
|
| 77 |
|
pkg_postinst() {
|
| 78 |
|
elog "All ${P} binaries have been renamed, in order"
|
| 79 |
|
elog "to avoid collisions with hmmer-3. For instance"
|
| 80 |
|
elog
|
| 81 |
|
elog " hmmalign -> hmmalign2"
|
| 82 |
|
elog
|
|
53 |
insinto /usr/share/hmmer
|
|
54 |
doins -r tutorial
|
| 83 |
55 |
}
|
